Scotty - Power Analysis for RNA Seq Experiments

Scotty is a tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to
achieve experimental aims.

At the start of every experiment, someone must ask the question, "How many reads do we need to sequence?" The answer to this question depends on how many of the
truely differentially expressed genes need to be detected. A greater number of genes will be found with an increase in the number of replicates
and an increase in how deeply each existing replicate is sequenced. These parameters are limited by the budget for performing the experiment.

The power that is available using a given number of reads will differ between experiments. Ideally, pilot runs of your experiment (small runs of at least two
replicates from one of your conditions) should be used to assess the amount of biological variance that is in the system you are studying, and the amount of
sequencing depth that is required to adequately measure the genes.
Alternatively, Scotty can be run on data from publicly-available datasets that are very close to your expected experiment
(species, library preparation protocol, sequencing technology, and read length).

The Matlab code that runs background calculations is available on github.
Please contact us if your require assistance.

Inputs

Pilot Data: Upload your own pilot data or used a stored dataset as a model for your experiment.
(?)